Re: expression heatmap displayer problem

Can you look in the tomcat logs. Do you see any errors? They should be
in $TOMCAT/logs. Usually catalina.out or localhost<DATE>.log.

I am guessing the data model used in that heatmap does not match your
data model.

Where did you get your Java file, HeatMapController.java? The link in
the docs is broken, I don't know where it lives now. If you look at that
file, what sort of query is it running? What sort of data does it
expect? You'll need the same data model OR update the code to use the
data model you have.

Re: expression heatmap displayer problem

1. I have rechecked the configurations following the
documentation in [1], and don't found any problem.

2. The associated files were also at the proper location. And
these files also uploaded at github [3].

3. I have put some debug phrase in the file heatMap.jsp [4] and
HeatMapController.java [5], and then re-built the webapp and
released without any error message. And then I uploaded one gene
list and checked the logs files located at
apache-tomcat-7.0.85/logs/ and didn't find these debug words "I
am" in the log files.

So, I suspect that the heatmap widget wasn't invoked any more
after I uploaded the gene list. How can I debug next?

Can you look in the tomcat logs. Do you see any errors? They
should be in $TOMCAT/logs. Usually catalina.out or
localhost<DATE>.log.

I am guessing the data model used in that heatmap does not match
your data model.

Where did you get your Java file, HeatMapController.java? The link
in the docs is broken, I don't know where it lives now. If you
look at that file, what sort of query is it running? What sort of
data does it expect? You'll need the same data model OR update the
code to use the data model you have.

Re: expression heatmap displayer problem

Hi Julie,

I forgot to run "git push" after "git add" and "git commit". Now the
modified source has been pushed.

Thank you and best,

Pengcheng

On 2018-5-1 15:54, Julie Sullivan wrote:

> Pengcheng
>
> Did you upload the struts config file you are using to github?
>
> https://github.com/pengchy/intermine/blob/master/testmine/webapp/resources/struts-config-model.xml>
>
> https://github.com/pengchy/intermine/blob/master/testmine/webapp/resources/tiles-defs-model.xml>
>
> Because they do not contain config for the heatmap. Maybe you could
> upload just so I can check the syntax.
>
> Julie
>
> On 05/01/2018 08:45 AM, Pengcheng Yang wrote:
>> Hi Julie and Sam,
>>
>> Thank you all for the suggestions.
>>
>> 1. I have rechecked the configurations following the documentation in
>> [1], and don't found any problem.
>>
>> 2. The associated files were also at the proper location. And these
>> files also uploaded at github [3].
>>
>> 3. I have put some debug phrase in the file heatMap.jsp [4] and
>> HeatMapController.java [5], and then re-built the webapp and released
>> without any error message. And then I uploaded one gene list and
>> checked the logs files located at apache-tomcat-7.0.85/logs/ and
>> didn't find these debug words "I am" in the log files.
>>
>> So, I suspect that the heatmap widget wasn't invoked any more after I
>> uploaded the gene list. How can I debug next?
>>
>> [1]
>> http://intermine.readthedocs.io/en/latest/webapp/third-party-tools/heatmap/>>
>> [2] locations of several files:
>>
>> webapp/resources/webapp/model/heatMap.jsp
>>
>> webapp/src/org/testmine/web/ExpressionResults.java
>> webapp/src/org/testmine/web/HeatMapController.java
>> webapp/src/org/testmine/web/TestMineUtil.java
>>
>> [3] https://github.com/pengchy/intermine/tree/master/testmine/>>
>> [4] the following debug phrases were put at the line 5-7 in
>> heatMap.jsp just after the
>>
>> <%@ page import="java.net.URLEncoder" language="java" %>
>> <script type="text/javascript">
>> document.writeln("I am here");
>> </script>
>>
>> <!-- heatMap.jsp -->
>>
>> [5] the following debug phrases were put at the line 51-53
>>
>> public class HeatMapController extends TilesAction
>> {
>>
>> public static void main(String[] args) {
>> System.out.println("I am at HeatMapController!");
>> }
>>
>> protected static final Logger LOG =
>> Logger.getLogger(HeatMapController.class);
>>
>> ---------------
>>
>> Thank you and best,
>>
>> Pengcheng
>>
>>
>>
>> On 2018-4-30 16:37, Julie Sullivan wrote:
>>> Hi Pengcheng,
>>>
>>> Can you look in the tomcat logs. Do you see any errors? They should
>>> be in $TOMCAT/logs. Usually catalina.out or localhost<DATE>.log.
>>>
>>> I am guessing the data model used in that heatmap does not match
>>> your data model.
>>>
>>> Where did you get your Java file, HeatMapController.java? The link
>>> in the docs is broken, I don't know where it lives now. If you look
>>> at that file, what sort of query is it running? What sort of data
>>> does it expect? You'll need the same data model OR update the code
>>> to use the data model you have.
>>>
>>> Cheers
>>> Julie
>>>
>>> On 04/27/2018 03:25 PM, Pengcheng Yang wrote:
>>>> Hi Interminers,
>>>>
>>>> I am implementing expression heatmap displayer following the
>>>> documentation:
>>>> http://intermine.readthedocs.io/en/latest/webapp/third-party-tools/heatmap/.
>>>> I have successfully built and released the webapp WAR file. But
>>>> when I upload a gene list, the heatmap was not displayed. The steps
>>>> are as follows:
>>>>
>>>> 1. the Expression data model:
>>>>
>>>> <class name="RNASeqResult" is-interface="true">
>>>> <attribute name="expressionScore" type="java.lang.Double"/>
>>>> <reference name="gene" referenced-type="Gene"
>>>> reverse-reference="rnaSeqResults"/>
>>>> <reference name="sample" referenced-type="Sample"
>>>> reverse-reference="rnaSeqResults"/>
>>>> <collection name="dataSets" referenced-type="DataSet" />
>>>> </class>
>>>>
>>>> 2. I have modified the controller files and modified the
>>>> struts-config-model.xml, tiles-defs-model.xml and heatMap.jsp
>>>> files. All these files have been uploaded onto the github at:
>>>> https://github.com/pengchy/intermine/tree/master/testmine/webapp/>>>>
>>>> Could someone help me debug this problem or tell me how to debug.
>>>> Thank you!
>>>>
>>>> Best,
>>>>
>>>> Pengcheng Yang
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> dev mailing list
>>>> [hidden email]>>>> https://lists.intermine.org/mailman/listinfo/dev>>>>
>>>
>>
>

> Hi Julie,
>
> I forgot to run "git push" after "git add" and "git commit". Now the
> modified source has been pushed.
>
> Thank you and best,
>
> Pengcheng
>
>
> On 2018-5-1 15:54, Julie Sullivan wrote:
>> Pengcheng
>>
>> Did you upload the struts config file you are using to github?
>>
>> https://github.com/pengchy/intermine/blob/master/testmine/webapp/resources/struts-config-model.xml>>
>>
>> https://github.com/pengchy/intermine/blob/master/testmine/webapp/resources/tiles-defs-model.xml>>
>>
>> Because they do not contain config for the heatmap. Maybe you could
>> upload just so I can check the syntax.
>>
>> Julie
>>
>> On 05/01/2018 08:45 AM, Pengcheng Yang wrote:
>>> Hi Julie and Sam,
>>>
>>> Thank you all for the suggestions.
>>>
>>> 1. I have rechecked the configurations following the documentation in
>>> [1], and don't found any problem.
>>>
>>> 2. The associated files were also at the proper location. And these
>>> files also uploaded at github [3].
>>>
>>> 3. I have put some debug phrase in the file heatMap.jsp [4] and
>>> HeatMapController.java [5], and then re-built the webapp and released
>>> without any error message. And then I uploaded one gene list and
>>> checked the logs files located at apache-tomcat-7.0.85/logs/ and
>>> didn't find these debug words "I am" in the log files.
>>>
>>> So, I suspect that the heatmap widget wasn't invoked any more after I
>>> uploaded the gene list. How can I debug next?
>>>
>>> [1]
>>> http://intermine.readthedocs.io/en/latest/webapp/third-party-tools/heatmap/>>>
>>>
>>> [2] locations of several files:
>>>
>>> webapp/resources/webapp/model/heatMap.jsp
>>>
>>> webapp/src/org/testmine/web/ExpressionResults.java
>>> webapp/src/org/testmine/web/HeatMapController.java
>>> webapp/src/org/testmine/web/TestMineUtil.java
>>>
>>> [3] https://github.com/pengchy/intermine/tree/master/testmine/>>>
>>> [4] the following debug phrases were put at the line 5-7 in
>>> heatMap.jsp just after the
>>>
>>> <%@ page import="java.net.URLEncoder" language="java" %>
>>> <script type="text/javascript">
>>> document.writeln("I am here");
>>> </script>
>>>
>>> <!-- heatMap.jsp -->
>>>
>>> [5] the following debug phrases were put at the line 51-53
>>>
>>> public class HeatMapController extends TilesAction
>>> {
>>>
>>> public static void main(String[] args) {
>>> System.out.println("I am at HeatMapController!");
>>> }
>>>
>>> protected static final Logger LOG =
>>> Logger.getLogger(HeatMapController.class);
>>>
>>> ---------------
>>>
>>> Thank you and best,
>>>
>>> Pengcheng
>>>
>>>
>>>
>>> On 2018-4-30 16:37, Julie Sullivan wrote:
>>>> Hi Pengcheng,
>>>>
>>>> Can you look in the tomcat logs. Do you see any errors? They should
>>>> be in $TOMCAT/logs. Usually catalina.out or localhost<DATE>.log.
>>>>
>>>> I am guessing the data model used in that heatmap does not match
>>>> your data model.
>>>>
>>>> Where did you get your Java file, HeatMapController.java? The link
>>>> in the docs is broken, I don't know where it lives now. If you look
>>>> at that file, what sort of query is it running? What sort of data
>>>> does it expect? You'll need the same data model OR update the code
>>>> to use the data model you have.
>>>>
>>>> Cheers
>>>> Julie
>>>>
>>>> On 04/27/2018 03:25 PM, Pengcheng Yang wrote:
>>>>> Hi Interminers,
>>>>>
>>>>> I am implementing expression heatmap displayer following the
>>>>> documentation:
>>>>> http://intermine.readthedocs.io/en/latest/webapp/third-party-tools/heatmap/.
>>>>> I have successfully built and released the webapp WAR file. But
>>>>> when I upload a gene list, the heatmap was not displayed. The steps
>>>>> are as follows:
>>>>>
>>>>> 1. the Expression data model:
>>>>>
>>>>> <class name="RNASeqResult" is-interface="true">
>>>>> <attribute name="expressionScore" type="java.lang.Double"/>
>>>>> <reference name="gene" referenced-type="Gene"
>>>>> reverse-reference="rnaSeqResults"/>
>>>>> <reference name="sample" referenced-type="Sample"
>>>>> reverse-reference="rnaSeqResults"/>
>>>>> <collection name="dataSets" referenced-type="DataSet" />
>>>>> </class>
>>>>>
>>>>> 2. I have modified the controller files and modified the
>>>>> struts-config-model.xml, tiles-defs-model.xml and heatMap.jsp
>>>>> files. All these files have been uploaded onto the github at:
>>>>> https://github.com/pengchy/intermine/tree/master/testmine/webapp/>>>>>
>>>>> Could someone help me debug this problem or tell me how to debug.
>>>>> Thank you!
>>>>>
>>>>> Best,
>>>>>
>>>>> Pengcheng Yang
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> dev mailing list
>>>>> [hidden email]>>>>> https://lists.intermine.org/mailman/listinfo/dev>>>>>
>>>>
>>>
>>
>

Re: expression heatmap displayer problem

Hi Julie,

Great, it output the error message [1,2] after I upload one gene list. I
will debug it later.

Thank you!

Pengcheng

[1] error message from localhost.2018-05-01.log

May 01, 2018 5:12:40 PM org.apache.catalina.core.StandardWrapperValve invoke
SEVERE: Servlet.service() for servlet [action] in context with path
[/testmine] threw exception [javax.servlet.ServletException:
javax.servlet.jsp.JspException: ServletException in 'bagDetails.jsp':
javax.servlet.jsp.JspException: ServletException in
'/bagDisplayers.jsp': javax.servlet.jsp.JspException: Can't insert page
'heatMap.title' : The requested resource (/testmine/heatMap.title) is
not available] with root cause
javax.servlet.jsp.JspException: Can't insert page 'heatMap.title' : The
requested resource (/testmine/heatMap.title) is not available
at
org.apache.struts.tiles.taglib.InsertTag$InsertHandler.doEndTag(InsertTag.java:902)
at
org.apache.struts.tiles.taglib.InsertTag.doEndTag(InsertTag.java:465)
at
org.apache.jsp.bagDisplayers_jsp._jspx_meth_tiles_005finsert_005f0(bagDisplayers_jsp.java:417)
at
org.apache.jsp.bagDisplayers_jsp._jspx_meth_c_005fif_005f1(bagDisplayers_jsp.java:353)
at
org.apache.jsp.bagDisplayers_jsp._jspx_meth_c_005fforEach_005f1(bagDisplayers_jsp.java:309)
at
org.apache.jsp.bagDisplayers_jsp._jspx_meth_c_005fif_005f0(bagDisplayers_jsp.java:272)
at
org.apache.jsp.bagDisplayers_jsp._jspx_meth_c_005fforEach_005f0(bagDisplayers_jsp.java:232)
at
org.apache.jsp.bagDisplayers_jsp._jspService(bagDisplayers_jsp.java:121)
at
org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
at
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:439)
at
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:395)
at
org.apache.jasper.servlet.JspServlet.service(JspServlet.java:339)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at
org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:743)
at
org.apache.catalina.core.ApplicationDispatcher.doInclude(ApplicationDispatcher.java:603)
at
org.apache.catalina.core.ApplicationDispatcher.include(ApplicationDispatcher.java:542)
at
org.apache.jasper.runtime.JspRuntimeLibrary.include(JspRuntimeLibrary.java:905)
at
org.apache.jasper.runtime.PageContextImpl.doInclude(PageContextImpl.java:688)
at
org.apache.jasper.runtime.PageContextImpl.include(PageContextImpl.java:682)
at sun.reflect.GeneratedMethodAccessor180.invoke(Unknown Source)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at
org.apache.struts.tiles.TilesUtilImpl.doInclude(TilesUtilImpl.java:129)
at org.apache.struts.tiles.TilesUtil.doInclude(TilesUtil.java:152)
at
org.apache.struts.tiles.taglib.InsertTag.doInclude(InsertTag.java:764)
at
org.apache.struts.tiles.taglib.InsertTag$InsertHandler.doEndTag(InsertTag.java:896)
at
org.apache.struts.tiles.taglib.InsertTag.doEndTag(InsertTag.java:465)
at
org.apache.jsp.bagDetails_jsp._jspx_meth_tiles_005finsert_005f2(bagDetails_jsp.java:2234)
at
org.apache.jsp.bagDetails_jsp._jspx_meth_c_005fif_005f3(bagDetails_jsp.java:2192)
at
org.apache.jsp.bagDetails_jsp._jspx_meth_c_005fwhen_005f0(bagDetails_jsp.java:536)
at
org.apache.jsp.bagDetails_jsp._jspx_meth_c_005fchoose_005f0(bagDetails_jsp.java:353)
at
org.apache.jsp.bagDetails_jsp._jspService(bagDetails_jsp.java:223)
at
org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
at
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:439)
at
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:395)
at
org.apache.jasper.servlet.JspServlet.service(JspServlet.java:339)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at
org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:743)
at
org.apache.catalina.core.ApplicationDispatcher.doInclude(ApplicationDispatcher.java:603)
at
org.apache.catalina.core.ApplicationDispatcher.include(ApplicationDispatcher.java:542)
at
org.apache.jasper.runtime.JspRuntimeLibrary.include(JspRuntimeLibrary.java:905)
at
org.apache.jasper.runtime.PageContextImpl.doInclude(PageContextImpl.java:688)
at
org.apache.jasper.runtime.PageContextImpl.include(PageContextImpl.java:682)
at sun.reflect.GeneratedMethodAccessor180.invoke(Unknown Source)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at
org.apache.struts.tiles.TilesUtilImpl.doInclude(TilesUtilImpl.java:129)
at org.apache.struts.tiles.TilesUtil.doInclude(TilesUtil.java:152)
at
org.apache.struts.tiles.taglib.InsertTag.doInclude(InsertTag.java:764)
at
org.apache.struts.tiles.taglib.InsertTag$InsertHandler.doEndTag(InsertTag.java:896)
at
org.apache.struts.tiles.taglib.InsertTag.doEndTag(InsertTag.java:465)
at
org.apache.jsp.layout_jsp._jspx_meth_tiles_005fget_005f1(layout_jsp.java:1239)
at org.apache.jsp.layout_jsp._jspService(layout_jsp.java:254)
at
org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
at
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:439)
at
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:395)
at
org.apache.jasper.servlet.JspServlet.service(JspServlet.java:339)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at
org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at
org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:743)
at
org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:485)
at
org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:410)
at
org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:337)
at
org.apache.struts.action.RequestProcessor.doForward(RequestProcessor.java:1083)
at
org.apache.struts.tiles.TilesRequestProcessor.doForward(TilesRequestProcessor.java:295)
at
org.apache.struts.tiles.TilesRequestProcessor.processTilesDefinition(TilesRequestProcessor.java:271)
at
org.apache.struts.tiles.TilesRequestProcessor.internalModuleRelativeForward(TilesRequestProcessor.java:370)
at
org.apache.struts.action.RequestProcessor.processForward(RequestProcessor.java:566)
at
org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:212)
at
org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913)
at
org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:449)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:624)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at
org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at
org.intermine.web.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:139)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:110)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
at
org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:962)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:445)
at
org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1115)
at
org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:637)
at
org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.doRun(AprEndpoint.java:2555)
at
org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.run(AprEndpoint.java:2544)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at
org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:748)

[2] error message from catalina.out

78424 [http-apr-10.4.0.17-8080-exec-86] ERROR
org.apache.struts.tiles.taglib.InsertTag - ServletException in
'bagDetails.jsp': javax.servlet.jsp.JspException: ServletException in
'/bagDisplayers.jsp': javax.servlet.jsp.JspException: Can't insert page
'heatMap.title' : The requested resource (/testmine/heatMap.title) is
not available
org.apache.jasper.JasperException: javax.servlet.ServletException:
javax.servlet.jsp.JspException: ServletException in
'/bagDisplayers.jsp': javax.servlet.jsp.JspException: Can't insert page
'heatMap.title' : The requested resource (/testmine/heatMap.title) is
not available
at
org.apache.jasper.servlet.JspServletWrapper.handleJspException(JspServletWrapper.java:597)
at
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:462)
at
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:395)
at
org.apache.jasper.servlet.JspServlet.service(JspServlet.java:339)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at
org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:743)
at
org.apache.catalina.core.ApplicationDispatcher.doInclude(ApplicationDispatcher.java:603)
at
org.apache.catalina.core.ApplicationDispatcher.include(ApplicationDispatcher.java:542)
at
org.apache.jasper.runtime.JspRuntimeLibrary.include(JspRuntimeLibrary.java:905)
at
org.apache.jasper.runtime.PageContextImpl.doInclude(PageContextImpl.java:688)
at
org.apache.jasper.runtime.PageContextImpl.include(PageContextImpl.java:682)
at sun.reflect.GeneratedMethodAccessor180.invoke(Unknown Source)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at
org.apache.struts.tiles.TilesUtilImpl.doInclude(TilesUtilImpl.java:129)
at org.apache.struts.tiles.TilesUtil.doInclude(TilesUtil.java:152)
at
org.apache.struts.tiles.taglib.InsertTag.doInclude(InsertTag.java:764)
at
org.apache.struts.tiles.taglib.InsertTag$InsertHandler.doEndTag(InsertTag.java:896)
at
org.apache.struts.tiles.taglib.InsertTag.doEndTag(InsertTag.java:465)
at
org.apache.jsp.layout_jsp._jspx_meth_tiles_005fget_005f1(layout_jsp.java:1239)
at org.apache.jsp.layout_jsp._jspService(layout_jsp.java:254)
at
org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
at
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:439)
at
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:395)
at
org.apache.jasper.servlet.JspServlet.service(JspServlet.java:339)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at
org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at
org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:743)
at
org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:485)
at
org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:410)
at
org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:337)
at
org.apache.struts.action.RequestProcessor.doForward(RequestProcessor.java:1083)
at
org.apache.struts.tiles.TilesRequestProcessor.doForward(TilesRequestProcessor.java:295)
at
org.apache.struts.tiles.TilesRequestProcessor.processTilesDefinition(TilesRequestProcessor.java:271)
at
org.apache.struts.tiles.TilesRequestProcessor.internalModuleRelativeForward(TilesRequestProcessor.java:370)
at
org.apache.struts.action.RequestProcessor.processForward(RequestProcessor.java:566)
at
org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:212)
at
org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913)
at
org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:449)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:624)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at
org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at
org.intermine.web.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:139)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:110)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
at
org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:962)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:445)
at
org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1115)
at
org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:637)
at
org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.doRun(AprEndpoint.java:2555)
at
org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.run(AprEndpoint.java:2544)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at
org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:748)
Caused by: javax.servlet.ServletException:
javax.servlet.jsp.JspException: ServletException in
'/bagDisplayers.jsp': javax.servlet.jsp.JspException: Can't insert page
'heatMap.title' : The requested resource (/testmine/heatMap.title) is
not available
at
org.apache.jasper.runtime.PageContextImpl.doHandlePageException(PageContextImpl.java:912)
at
org.apache.jasper.runtime.PageContextImpl.handlePageException(PageContextImpl.java:845)
at
org.apache.jsp.bagDetails_jsp._jspService(bagDetails_jsp.java:238)
at
org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
at
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:439)
... 69 more
Caused by: org.apache.jasper.JasperException:
javax.servlet.ServletException: javax.servlet.jsp.JspException: Can't
insert page 'heatMap.title' : The requested resource
(/testmine/heatMap.title) is not available
at
org.apache.jasper.servlet.JspServletWrapper.handleJspException(JspServletWrapper.java:597)
at
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:462)
at
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:395)
at
org.apache.jasper.servlet.JspServlet.service(JspServlet.java:339)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at
org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:743)
at
org.apache.catalina.core.ApplicationDispatcher.doInclude(ApplicationDispatcher.java:603)
at
org.apache.catalina.core.ApplicationDispatcher.include(ApplicationDispatcher.java:542)
at
org.apache.jasper.runtime.JspRuntimeLibrary.include(JspRuntimeLibrary.java:905)
at
org.apache.jasper.runtime.PageContextImpl.doInclude(PageContextImpl.java:688)
at
org.apache.jasper.runtime.PageContextImpl.include(PageContextImpl.java:682)
at sun.reflect.GeneratedMethodAccessor180.invoke(Unknown Source)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at
org.apache.struts.tiles.TilesUtilImpl.doInclude(TilesUtilImpl.java:129)
at org.apache.struts.tiles.TilesUtil.doInclude(TilesUtil.java:152)
at
org.apache.struts.tiles.taglib.InsertTag.doInclude(InsertTag.java:764)
at
org.apache.struts.tiles.taglib.InsertTag$InsertHandler.doEndTag(InsertTag.java:896)
at
org.apache.struts.tiles.taglib.InsertTag.doEndTag(InsertTag.java:465)
at
org.apache.jsp.bagDetails_jsp._jspx_meth_tiles_005finsert_005f2(bagDetails_jsp.java:2234)
at
org.apache.jsp.bagDetails_jsp._jspx_meth_c_005fif_005f3(bagDetails_jsp.java:2192)
at
org.apache.jsp.bagDetails_jsp._jspx_meth_c_005fwhen_005f0(bagDetails_jsp.java:536)
at
org.apache.jsp.bagDetails_jsp._jspx_meth_c_005fchoose_005f0(bagDetails_jsp.java:353)
at
org.apache.jsp.bagDetails_jsp._jspService(bagDetails_jsp.java:223)
... 72 more
Caused by: javax.servlet.ServletException:
javax.servlet.jsp.JspException: Can't insert page 'heatMap.title' : The
requested resource (/testmine/heatMap.title) is not available
at
org.apache.jasper.runtime.PageContextImpl.doHandlePageException(PageContextImpl.java:916)
at
org.apache.jasper.runtime.PageContextImpl.handlePageException(PageContextImpl.java:845)
at
org.apache.jsp.bagDisplayers_jsp._jspService(bagDisplayers_jsp.java:135)
at
org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
at
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:439)
... 96 more
Caused by: javax.servlet.jsp.JspException: Can't insert page
'heatMap.title' : The requested resource (/testmine/heatMap.title) is
not available
at
org.apache.struts.tiles.taglib.InsertTag$InsertHandler.doEndTag(InsertTag.java:902)
at
org.apache.struts.tiles.taglib.InsertTag.doEndTag(InsertTag.java:465)
at
org.apache.jsp.bagDisplayers_jsp._jspx_meth_tiles_005finsert_005f0(bagDisplayers_jsp.java:417)
at
org.apache.jsp.bagDisplayers_jsp._jspx_meth_c_005fif_005f1(bagDisplayers_jsp.java:353)
at
org.apache.jsp.bagDisplayers_jsp._jspx_meth_c_005fforEach_005f1(bagDisplayers_jsp.java:309)
at
org.apache.jsp.bagDisplayers_jsp._jspx_meth_c_005fif_005f0(bagDisplayers_jsp.java:272)
at
org.apache.jsp.bagDisplayers_jsp._jspx_meth_c_005fforEach_005f0(bagDisplayers_jsp.java:232)
at
org.apache.jsp.bagDisplayers_jsp._jspService(bagDisplayers_jsp.java:121)
... 99 more

On 2018-5-1 16:39, Julie Sullivan wrote:

> Sorry! There was one bit left out of the documentation. You configured
> the heatmap correctly, we are just missing the bit that tells the
> report page to show the heatmap on gene pages.
>
> Here's what Sam does:
>
> https://github.com/LegumeFederation/peanutmine/blob/master/webapp/resources/webapp/WEB-INF/webconfig-model.xml#L77>
>
> Try that?
>
> And I will update the docs!
>
> On 05/01/2018 09:20 AM, Pengcheng Yang wrote:
>> Hi Julie,
>>
>> I forgot to run "git push" after "git add" and "git commit". Now the
>> modified source has been pushed.
>>
>> Thank you and best,
>>
>> Pengcheng
>>
>>
>> On 2018-5-1 15:54, Julie Sullivan wrote:
>>> Pengcheng
>>>
>>> Did you upload the struts config file you are using to github?
>>>
>>> https://github.com/pengchy/intermine/blob/master/testmine/webapp/resources/struts-config-model.xml>>>
>>>
>>> https://github.com/pengchy/intermine/blob/master/testmine/webapp/resources/tiles-defs-model.xml>>>
>>>
>>> Because they do not contain config for the heatmap. Maybe you could
>>> upload just so I can check the syntax.
>>>
>>> Julie
>>>
>>> On 05/01/2018 08:45 AM, Pengcheng Yang wrote:
>>>> Hi Julie and Sam,
>>>>
>>>> Thank you all for the suggestions.
>>>>
>>>> 1. I have rechecked the configurations following the documentation
>>>> in [1], and don't found any problem.
>>>>
>>>> 2. The associated files were also at the proper location. And these
>>>> files also uploaded at github [3].
>>>>
>>>> 3. I have put some debug phrase in the file heatMap.jsp [4] and
>>>> HeatMapController.java [5], and then re-built the webapp and
>>>> released without any error message. And then I uploaded one gene
>>>> list and checked the logs files located at
>>>> apache-tomcat-7.0.85/logs/ and didn't find these debug words "I am"
>>>> in the log files.
>>>>
>>>> So, I suspect that the heatmap widget wasn't invoked any more after
>>>> I uploaded the gene list. How can I debug next?
>>>>
>>>> [1]
>>>> http://intermine.readthedocs.io/en/latest/webapp/third-party-tools/heatmap/>>>>
>>>>
>>>> [2] locations of several files:
>>>>
>>>> webapp/resources/webapp/model/heatMap.jsp
>>>>
>>>> webapp/src/org/testmine/web/ExpressionResults.java
>>>> webapp/src/org/testmine/web/HeatMapController.java
>>>> webapp/src/org/testmine/web/TestMineUtil.java
>>>>
>>>> [3] https://github.com/pengchy/intermine/tree/master/testmine/>>>>
>>>> [4] the following debug phrases were put at the line 5-7 in
>>>> heatMap.jsp just after the
>>>>
>>>> <%@ page import="java.net.URLEncoder" language="java" %>
>>>> <script type="text/javascript">
>>>> document.writeln("I am here");
>>>> </script>
>>>>
>>>> <!-- heatMap.jsp -->
>>>>
>>>> [5] the following debug phrases were put at the line 51-53
>>>>
>>>> public class HeatMapController extends TilesAction
>>>> {
>>>>
>>>> public static void main(String[] args) {
>>>> System.out.println("I am at HeatMapController!");
>>>> }
>>>>
>>>> protected static final Logger LOG =
>>>> Logger.getLogger(HeatMapController.class);
>>>>
>>>> ---------------
>>>>
>>>> Thank you and best,
>>>>
>>>> Pengcheng
>>>>
>>>>
>>>>
>>>> On 2018-4-30 16:37, Julie Sullivan wrote:
>>>>> Hi Pengcheng,
>>>>>
>>>>> Can you look in the tomcat logs. Do you see any errors? They
>>>>> should be in $TOMCAT/logs. Usually catalina.out or
>>>>> localhost<DATE>.log.
>>>>>
>>>>> I am guessing the data model used in that heatmap does not match
>>>>> your data model.
>>>>>
>>>>> Where did you get your Java file, HeatMapController.java? The link
>>>>> in the docs is broken, I don't know where it lives now. If you
>>>>> look at that file, what sort of query is it running? What sort of
>>>>> data does it expect? You'll need the same data model OR update the
>>>>> code to use the data model you have.
>>>>>
>>>>> Cheers
>>>>> Julie
>>>>>
>>>>> On 04/27/2018 03:25 PM, Pengcheng Yang wrote:
>>>>>> Hi Interminers,
>>>>>>
>>>>>> I am implementing expression heatmap displayer following the
>>>>>> documentation:
>>>>>> http://intermine.readthedocs.io/en/latest/webapp/third-party-tools/heatmap/.
>>>>>> I have successfully built and released the webapp WAR file. But
>>>>>> when I upload a gene list, the heatmap was not displayed. The
>>>>>> steps are as follows:
>>>>>>
>>>>>> 1. the Expression data model:
>>>>>>
>>>>>> <class name="RNASeqResult" is-interface="true">
>>>>>> <attribute name="expressionScore" type="java.lang.Double"/>
>>>>>> <reference name="gene" referenced-type="Gene"
>>>>>> reverse-reference="rnaSeqResults"/>
>>>>>> <reference name="sample" referenced-type="Sample"
>>>>>> reverse-reference="rnaSeqResults"/>
>>>>>> <collection name="dataSets" referenced-type="DataSet" />
>>>>>> </class>
>>>>>>
>>>>>> 2. I have modified the controller files and modified the
>>>>>> struts-config-model.xml, tiles-defs-model.xml and heatMap.jsp
>>>>>> files. All these files have been uploaded onto the github at:
>>>>>> https://github.com/pengchy/intermine/tree/master/testmine/webapp/>>>>>>
>>>>>> Could someone help me debug this problem or tell me how to debug.
>>>>>> Thank you!
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>> Pengcheng Yang
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> dev mailing list
>>>>>> [hidden email]>>>>>> https://lists.intermine.org/mailman/listinfo/dev>>>>>>
>>>>>
>>>>
>>>
>>
>